Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes

Abstract

Comparisons of complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera to six published grass chloroplast genomes reveal that gene content and order are similar but two microstructural changes have occurred. First, the expansion of the IR at the SSC/IRa boundary that duplicates a portion of the 5' end of ndhH is restricted to the three genera of the subfamily Pooideae (Agrostis, Hordeum and Triticum). Second, a 6 bp deletion in ndhK is shared by Agrostis, Hordeum, Oryza and Triticum, and this event supports the sister relationship between the subfamilies Erhartoideae and Pooideae. Repeat analysis identified 19-37 direct and inverted repeats 30 bp or longer with a sequence identity of at least 90%. Seventeen of the 26 shared repeats are found in all the grass chloroplast genomes examined and are located in the same genes or intergenic spacer (IGS) regions. Examination of simple sequence repeats (SSRs) identified 16-21 potential polymorphic SSRs. Five IGS regions have 100% sequence identity among Zea mays, Saccharum officinarum and Sorghum bicolor, whereas no spacer regions were identical among Oryza sativa, Triticum aestivum, H. vulgare and A. stolonifera despite their close phylogenetic relationship. Alignment of EST sequences and DNA coding sequences identified six C-U conversions in both Sorghum bicolor and H. vulgare but only one in A. stolonifera. Phylogenetic trees based on DNA sequences of 61 protein-coding genes of 38 taxa using both maximum parsimony and likelihood methods provide moderate support for a sister relationship between the subfamilies Erhartoideae and Pooideae.

Fig. 1

Gene map of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera chloroplast genomes. The thick lines indicate the extent of the inverted repeats (IRa and IRb), which separate the genome into small (SSC) and large (LSC) single copy regions. Genes on the outside of the map are transcribed in the clockwise direction and genes on the inside of the map are transcribed in the counterclockwise direction

Fig. 2

Histogram showing the number of repeated sequences ≥30 bp long with a sequence identity ≥90% in nine grass chloroplast genomes

Fig. 3

Histogram showing pairwise sequence divergence of the intergenic spacer regions of rice (Oryza sativa), wheat (Triticum aestivum) barley (Hordeum vulgare) and bentgrass (Agrostis stolonifera) chloroplast genomes. Comparisons of 19 most variable intergenic regions with less than 80% average sequence identity. The values plotted in this histogram come from Supplementary Table 1, which shows percent sequence identities for all intergenic spacer regions. The plotted values were converted from percent identity to sequence divergence on a scale from 0 to 1 and included on the Y-axis. Asterisk indicates regions that are in the top 25 most variable intergenic spacer regions in Solanaceae (adapted from Daniell et al. 2006), plus indicates regions that are in the top 25 most variable intergenic spacer regions in Asteraceae (adapted from Timme et al. 2007)

Fig. 4

Histogram showing pairwise sequence divergence of the intergenic spacer regions of maize (Zea mays), sugarcane (Saccharum officinarum) and sorghum (Sorghum bicolor) chloroplast genomes. Comparisons of the nine most variable intergenic spacer regions with less than 80% average sequence identity. The values plotted in this histogram come from Supplementary Table 2, which shows percent sequence identities for all intergenic spacer regions. The plotted values were converted from percent identity to sequence divergence on a scale from 0 to 1 and included on the Y-axis. Asterisk indicates regions that are in the top 25 most variable intergenic spacer regions in Solanaceae (adapted from Daniell et al. 2006), plus indicates regions that are in the top 25 most variable intergenic spacer regions in Asteraceae (adapted from Timme et al. 2007)

Fig. 5

Phylogenetic tree of 38 taxa based on 61 plastid protein-coding genes using maximum parsimony. The tree has a length of 62,437, a consistency index of 0.407 (excluding uninformative characters) and a retention index of 0.627. Numbers above node indicate number of changes along each branch and numbers below nodes are bootstrap support values. Ordinal and higher level group names follow APG II (2003). Taxa in red are the new genomes reported in this paper

Fig. 6

Phylogenetic tree of 38 taxa based on 61 plastid protein-coding genes using maximum likelihood. The tree has a ML value of −lnL = 348086.2268. Numbers at nodes are bootstrap support values 50%. Ordinal and higher level group names follow APG II (2003). Taxa in red are the new genomes reported in this paper